GNU R utilities from Harvard School of Public Health Bioinformatics
This GNU R package contains the following functions:
chb_utils-package chb_utils
annotate_df Annotate Dataframe containing Ensembl IDs with Gene
Symbols and Descriptions
boxplotoutliers Cel file IDs of intensity boxplot outlier arrays (in
characters).
chb_utils chb_utils
col2rownames add a column to a dataframe consisting of the
current rownames
convertIDs Get other Ids for genes in the same order
create_report Create report of QC
getTFpairs Get mouse TF-target pairs from opossum database
get_biomart Get biomart annotation from id
ggheatmap generate a heatmap + dendrograms, ggplot2 style
ggheatmap.show Display a ggheatmap
ggplotDispEsts Plot Dispersion Estimates - nicer ggplot version of
DESeq graph
mds Plot MDS
mdsplot.RGset MDS (MultiDimensional Scaling) Plots
nuseoutliers Cel file IDs of intensity NUSE outlier arrays (in
characters).
PCAplot.cds Pairwise Principal Component Analysis Plots of
CountDataSet objects
PCAplot.eset Pairwise Principal Component Analysis Plots
Plots the differntially expressed genes on an MA
plotDE plot, ggplot style If adjusted pvalues are present,
colors those that pass cutoff red
plot_dendro ggplot based dendrogram plot
print_enrichGO Clean and print results from enrichGO
Plots the pvalue quantiles against the uniform
qqplot_JH distribution. If adjusted pvalues are present,
colors those that pass cutoff red
rleoutliers Cel file IDs of intensity RLE outlier arrays (in
characters).
row2colnames add a column to a dataframe consisting of the
current rownames
runGO Run GO using clusterprofiler
variance_by_component Plot PC importance
volcano_density_plot Create volcano plot from log2FC and adjusted pvalues
data frame
write_report Write report of QC
